SMTL ID : 5ykp.1

Human methionine aminopeptidase type 1b (F309M mutant) in complex with ovalicin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

3 x CO: COBALT (II) ION(Non-covalent)

CO.1: 7 residues within 4Å: Chain A: D.152, H.215, T.246, E.248, E.279 Ligands: CO.2, OVA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.152, A:H.215, A:E.248, A:E.279, H2O.1 CO.2: 4 residues within 4Å: Chain A: D.141, D.152, E.279 Ligands: CO.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.141, A:D.152, A:E.279, H2O.1, H2O.4 CO.3: 4 residues within 4Å: Chain A: E.40, Y.107, Y.108, H.222 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.107, A:H.222, H2O.4

1 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: S.117, V.118, N.119, V.121, S.275 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.117, A:N.119, A:V.121, A:S.275, H2O.8

1 x OVA: 3,4-DIHYDROXY-2-METHOXY-4-METHYL-3-[2-METHYL-3-(3-METHYL-BUT-2-ENYL) -OXIRANYL]-CYCLOHEXANONE(Covalent)

OVA.5: 12 residues within 4Å: Chain A: P.104, Y.107, H.124, Y.212, C.213, H.215, M.221, H.222, E.248, M.250, W.265 Ligands: CO.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.104, A:Y.107, A:Y.107, A:H.222, A:W.265 Hydrogen bonds: A:C.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pillalamarri, V. et al., Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis. Biochem. J. (2019)

Release Date

2018-10-17

Peptides

Methionine aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 1